System and methods for determining molecules using mass spectrometry and related techniques

ABSTRACT

The present invention generally relates to mass spectrometry and related techniques, and in some cases, to determining single species using mass spectrometry. In certain instances, polymers such as DNA or RNA can also be sequenced. Certain embodiments of the invention relate to passing a polymer, such as DNA, RNA, a protein, a polypeptide, a polysaccharide, etc., through a pore and cleaving the polymer in sequence. For instance, the polymer may be cleaved using a laser or an electric field. In some embodiments, a property of at least one subunit of a polymer is determined using mass spectrometry. In some embodiments, a single ion (which may be a subunit of a polymer, or an ion based on another species) can be isolated in a mass spectrometer and a signal generated from the single ion.

RELATED APPLICATIONS

This application is a national stage filing under 35 U.S.C. §371 of PCTApl. No. PCT/US2009/004400, filed Jul. 30, 2009, entitled “System andMethods for Determining Molecules Using Mass Spectrometry and RelatedTechniques,” which claims the benefit of U.S. Pat. Apl. Ser. No.61/085,480, filed Aug. 1, 2008, entitled “System and Methods forDetermining Molecules using Mass Spectrometry and Related Techniques,incorporated herein by reference.

FIELD OF THE INVENTION

The present invention generally relates to mass spectrometry and relatedtechniques, and in some cases, to determining single species using massspectrometry. In certain instances, polymers such as DNA or RNA can alsobe sequenced.

BACKGROUND OF THE INVENTION

Deoxyribonucleic acids (DNA), ribonucleic acids (RNA), and proteinscomprise linear polymers which often have particular sequences ofmonomer units. High speed and low cost methods for determining thesequence of each of these types of molecules are desired, for example,to assist basic biological studies and the development of health caseapplications, among other goals. The demand for sequencing is perhapshighest with DNA, and conventional DNA sequencing methods often requiremultiple copies of the target sequence and chemical synthesis reactions.The sequencing speed depends on factors such as the rate of suchchemical reactions, or the cost of the necessary chemical reagents andthe labor and energy needed to carry out the reactions.

SUMMARY OF THE INVENTION

The present invention generally relates to mass spectrometry and relatedtechniques, and in some cases, to determining single species using massspectrometry. In certain instances, polymers such as DNA or RNA can alsobe sequenced. The subject matter of the present invention involves, insome cases, interrelated products, alternative solutions to a particularproblem, and/or a plurality of different uses of one or more systemsand/or articles.

In one aspect, the invention is directed to a method. According to afirst set of embodiments, the method includes acts of passing anpolynucleotide through a non-naturally occurring pore having a diameterof less than about 1 micrometer, and cleaving the polynucleotide insequence. In another set of embodiments, the method includes acts ofpassing an polynucleotide through a non-naturally occurring pore havinga diameter of less than about 1 micrometer, and cleaving thepolynucleotide using a laser or an electric field.

The method, in accordance with yet another set of embodiments, includesacts of isolating a single ion in a mass spectrometer, generating asignal in the mass spectrometer using the single ion, and obtaining amass spectrograph based on the signal, indicative of the single ion. Instill another set of embodiments, the method includes acts of passing apolymer through a pore having a diameter of less than about 1micrometer, and determining a property of at least one subunit of thepolymer using mass spectrometry.

In one set of embodiments, the method includes acts of passing a polymerthrough a pore having a diameter of less than about 1 micrometer,sequentially cleaving the polymer as it passes through the pore toproduce a plurality of fragments, and ionizing one or more of thefragments. In another set of embodiments, the method includes acts ofpassing a single molecule through a pore having a diameter of less thanabout 1 micrometer, creating at least one ion from the single molecule,and determining a property of the at least one ion.

The invention is directed to a system, in another aspect. According toone set of embodiments, the system includes a pore having a diameter ofless than about 1 micrometer, separating a low-pressure chamber and asample chamber, a particle source configured to direct particles in thelow-pressure chamber towards the pore, and a mass detection unitconfigured to determine ions produced within the low-pressure chamber.

Other aspects, embodiments and features of the invention will becomeapparent from the following detailed description when considered inconjunction with the accompanying drawings. The accompanying figures areschematic and are not intended to be drawn to scale. For purposes ofclarity, not every component is labeled in every figure, nor is everycomponent of each embodiment of the invention shown where illustrationis not necessary to allow those of ordinary skill in the art tounderstand the invention. All patent applications and patentsincorporated herein by reference are incorporated by reference in theirentirety. In case of conflict, the present specification, includingdefinitions, will control.

BRIEF DESCRIPTION OF THE DRAWINGS

Non-limiting embodiments of the present invention will be described byway of example with reference to the accompanying figures, which areschematic and are not intended to be drawn to scale. In the figures,each identical or nearly identical component illustrated is typicallyrepresented by a single numeral. For the purposes of clarity, not everycomponent is labeled in every figure, nor is every component of eachembodiment of the invention shown where illustration is not necessary toallow those of ordinary skill in the art to understand the invention. Inthe figures:

FIG. 1 shows the formation of a pore in a bilayer membrane, inaccordance with various embodiments of the invention;

FIG. 2 shows a mass spectrometer device configured with a pore, inaccordance with various embodiments of the invention;

FIG. 3 shows the translocation of a polymer through a pore and theionization and dissociation of a fragment of the polymer, in accordancewith various embodiments of the invention;

FIG. 4 illustrates the data output from sequencing DNA, in accordancewith various embodiments of the invention; and

FIG. 5 illustrates a mass spectrometer device in another embodiment ofthe invention.

DETAILED DESCRIPTION

The present invention generally relates to mass spectrometry and relatedtechniques, and in some cases, to determining single species using massspectrometry. In certain instances, polymers such as DNA or RNA can alsobe sequenced. Certain embodiments of the invention relate to passing apolymer, such as DNA, RNA, a protein, a polypeptide, a polysaccharide,etc., through a pore and cleaving the polymer in sequence. For instance,the polymer may be cleaved using a laser or an electric field. In someembodiments, a property of at least one subunit of a polymer isdetermined using mass spectrometry. In some embodiments, a single ion(which may be a subunit of a polymer, or an ion based on anotherspecies) can be isolated in a mass spectrometer and a signal generatedfrom the single ion.

One aspect of the present invention is generally directed to systems andmethods of sequencing a polymer using mass spectrometry and relatedtechniques. In some instances where the species is a polymer, thepolymer may be any polymer, including biopolymers or other organicpolymers. Non-limiting examples of biopolymers include a polynucleotide(e.g. DNA, RNA, etc.), a polypeptide (e.g. a protein, a hormone, etc.),a polysaccharide, (e.g. heparin, hyaluronic acid, glycogen, cellulose,chitin, etc.), or the like, as well as combinations of these. Thebiopolymer may be, for example, a naturally occurring molecule and/ormay be derived from a biological source, such as a cell, or thebiopolymer may be produced synthetically, for example on an automatedsynthesis machine. A biopolymer may also be a non-naturally occurringcomposition, for example a peptide-nucleic acid or a locked nucleicacid. The biopolymer may include other non-biopolymeric entities in somecases, for example fluorophores or other indicators, other polymers suchas poly(ethylene glycol), etc.

In one set of embodiments, a species, such as a biopolymer, is passedthrough a pore, and the species is determined via mass spectrometry.FIG. 5 illustrates an example of one embodiment of the invention, andshows polymer 12, such as DNA, in chamber 6. (Polymer 12 is used in thisexample as an illustrative embodiment; in other cases, however, otherspecies may be used as well, as discussed below.) Polymer 12 passes or“translocates” through pore 4 in membrane 7, emerges in chamber 8, whichmay be operated at reduced pressure in some cases. In some cases, anelectric field generated by electrodes 5 and 9 can be used to urge thepolymer through pore 4. Other techniques besides electric fields canalso be used to urge the polymer through the pore, as discussed below.In addition, in some cases, the pore may be of a size comparable to thewidth of the polymer (or other species) passing through the pore. As thepolymer emerges from the pore, monomers 13 are dissociated from polymer12. The monomers may be dissociated, for example, by an ionic beam, byan electric field, or the like, as discussed below. Monomer 12 can beaccelerated through mass spectrometer 19 using a magnetic field createdby magnetic region 10, before impinging on a detector 11, from which anoutput can be recorded.

Virtually any suitable species can be analyzed or determined in such asystem. The species may be a molecule or atom, or a plurality ofmolecules or atoms, some or all of which may be charged or uncharged,etc. For example, the species may be an organic molecule, an inorganicmolecule, a polymer (such as described above), etc. Accordingly, theinvention is not necessarily limited to only the determination ofpolymers. As used herein, the term “determining” generally refers to theanalysis of a species and/or signal, for example, quantitatively orqualitatively, and/or the detection of the presence or absence of thespecies or signals. For example, an ion may be determined by analyzingthe mass/charge ratio of the ion or otherwise obtaining a quantity fromwhich the molecular weight of the ion can be derived.

As mentioned, the species is passed through a pore in one set ofembodiments. A pores is generally a hole or an opening with a dimensionof less than about 1 micron in a membrane or other surface. In somecases, the membrane is continuous and solid, i.e., having only one porepresent, although in some embodiments of the invention, more than onepore may be present in a membrane. In some cases, the pore may have adimension less than about 500 nm, less than about 250 nm, or less thanabout 100 nm. In other cases, the pore may have a dimension less thanabout 50 nm, less than about 30 nm, less than about 15 nm, less thanabout 10 nm, less than about 5 nm, or less than about 2 nm. In someembodiments, the pore may have a dimension between about 1 nm and about5 nm, between about 4 nm and about 30 nm, between about 25 nm and about100 nm, etc. In some cases, the pore may have a dimension between about50 nm and about 250 nm, between about 200 nm and about 500 nm, betweenabout 400 nm and about 700 nm, between about 500 nm and about 1000 nm,etc. The actual size of the pore will vary, depending on the particularapplication, but will often be of dimensions comparable to dimensions ofthe species to be passed through the pore. Those of ordinary skill inthe art will be able to determine the dimension of pore through routineexperimentation using a variety of known techniques. In one embodiment,for instance, electron microscopy can be used to determine the size ofthe pore.

The pore may be of any shape and dimension. For instance, the pore canbe generally circular, octagonal, hexagonal, pentagonal, rectangular, ortriangular, etc. In some cases, the pore may have an irregular shape.The vertices of such structures may be vaguely defined, i.e. rounded, orsharp, or a combination of rounded and sharp. The sides or edges of thepore, on the surface or within the membrane comprising the pore may besimilar in length, for example in the case of a square, or may bedifferent, such as in a rectangle or non-ordered shape. In oneembodiment, the pore may have a general slit-like structure. The shapeor dimensions of the pore on one side of the membrane may be the same ordifferent from the shape or dimensions of the pore on the other side ofthe membrane. In one set of embodiments, the pore is non-naturallycreated. For instance, a pore may be created by creating a hole in amembrane, for example, using a laser.

In some aspects of the invention, a plurality of pores may be present inthe membrane. In some instances, each pore of the plurality or pores maybe similarly sized, and in other instances, the plurality of pores maycontain a range of pore sizes. As mentioned, the pore may be formed in amembrane. The membrane may be constructed out of any suitable material.Typically, the membrane is formed from materials suitable for preventingpassage of species therethrough, except for passage through the pore.For instance, the membrane may be constructed of solid state and/orpolymeric and/or ceramic materials, e.g. inorganic and organicmaterials, oxides, films, etc. Such materials are known to those skilledin the art. Specific, non-limiting examples include silicon, germanium,and compounds comprising silicon, such as silicon carbide and siliconnitride. The materials used may be a conductor in some cases, such asgold, palladium, platinum, copper, nickel, aluminum, iron, silver, etc.Polymeric materials may also be used, such as photoresists and plastics,e.g. PMMA, epoxies, polyethylene, polypropylene, etc. In otherinstances, conducting polymers exemplified by polythiophene andpolypyrrole can be used. In certain embodiments, one side of themembrane comprises silicon nitride and the other side comprises ametalized surface. In one embodiment, the silicon nitride side of themembrane is exposed to aqueous solution and the metalized side isexposed to an atmosphere of lower pressure, i.e. a vacuum.

In some instances, a carbon nanotube may be used to form a pore. Acarbon nanotube pore may be formed, for example, by embedding the carbonnanotube within a material (e.g., glass, silica, or other materials suchas those described herein) and sectioning the material such that amembrane is formed containing a carbon nanotube pore. In some instances,ions or molecules may be passed through the interior of the carbonnanotube. The carbon nanotube may have any suitable diameter, e.g.,having an average diameter of less than about 500 nm, less than about250 nm, or less than about 100 nm. In other cases, the pore may have adimension less than about 50 nm, less than about 30 nm, less than about15 nm, less than about 10 nm, less than about 5 nm, or less than about 2nm. In some embodiments, the pore may have a dimension between about 1nm and about 5 nm, between about 4 nm and about 30 nm, between about 25nm and about 100 nm, etc. The carbon nanotube may be single-walled ormultiwalled. Methods for synthesizing a carbon nanotube are known in theart.

In one embodiment, the pore may be a hole in an otherwise continuousthin membrane made of a solid material. A membrane, as can be seen inthe example of FIG. 1, may comprise a layer of a solid-state insulatorsuch a silicon nitride or silicon dioxide 1 and a layer of a metalconductor such as gold or platinum 2. A variety of techniques are knownin the art for fabricating pores such as ion beam sculpting andelectron-beam lithography followed by etching. FIG. 1 illustrates onemethod using a transmission electron beam 1 to obliterate a membranecomprising an insulator 2 and a conductor 3 to form a pore 4. Thethickness of each material layer comprising the membrane may be between5 nm and 100 nm. In some instances a layer may be less than about 2 nm,less than about 5 nm, less than about 10 nm, less than about 20 nm, lessthan about 30 nm, less than about 50 nm, less than about 75 nm, lessthan about 100 nm, less than about 150 nm, less than about 200 nm, etc.In other instances, the thickness of the layer may be between about 2 nmto 10 nm, between about 5 nm to 20 nm, between about 10 nm to 30 nm,between about 20 nm to 50 nm, between about 30 nm to 75 nm, betweenabout 50 nm to 100 nm, between about 75 nm to 150 nm, between about 100nm to 200 nm, etc. In some embodiments, the layer may be greater than200 nm thick. The conductor layer constitutes an electrode, thepotential of which is controlled. The conducting side of the membranemay be sealed within a vacuum chamber that can house a mass spectrometeras can be seen in FIG. 2.

In some aspects, the pore separates a sample chamber 6 from a reducedpressure chamber 8, i.e. a vacuum chamber. The pressure change betweenthe two chambers may be, for example a change of 25%, 50%, or 75% of thelower pressure chamber, relative to the higher pressure chamber. In somecases, the pressure change may be of several orders of magnitude. Forinstance, the higher pressure chamber may be approximately atatmospheric pressure while the lower pressure chamber may have apressure of less about than 1 mmHg, less than about 0.1 mmHg, or lessthan about 0.01 mmHg. Such changes in pressure can be created, forexample, using suitable pressure or vacuum pumps in fluidiccommunication with either side of the membrane defining the pore.

In some embodiments, the sample chamber 6 contains an aqueous solutionin which candidate molecules are dissolved. The temperature and pressureof the chamber may controlled. The solution can contain a variety ofadditives including salts, buffers, and chaotropic agents such asguanidine hydrochloride, urea, or organic solvents. In certainembodiments, the temperature, chemical composition, and/or pH of thesample chamber solution can be adjusted to create conditions conduciveto denaturation of molecules, for example of proteins and nucleic acids.In some embodiments, a reduced pressure chamber 8 exists on the side ofthe membrane and pore opposite of the sample chamber 6. It is to beunderstood that the term “vacuum” as used herein does not necessarilyimply a perfect vacuum and in most instances refers to a region of lowerpressure relative to another region. In some embodiments the vacuum is apressure of less than about 760 mmHg, less than about 500 mmHg, lessthan about 100 mmHg, less than about 10 mmHg, less than about 1 mmHg,less than about 0.1 mmHg, less than about 0.001 mmHg, less than about 50microns of Hg, less than about 10 microns of Hg, less than about 1micron of Hg, or less than about 0.001 microns of Hg. It is understoodthat 760 mmHg is equivalent to 101325 Pa.

In another aspect of the invention, the pore or device comprising thepore is configured to allow molecules to traverse the pore as seen inFIG. 3. In some embodiments, the traversal of molecules occurs one at atime and in single file fashion. “Single file” is defined as eachmonomer moving through a pore one at a time and in sequence. A polymerpassing through a pore in single file fashion typically will not foldupon itself within the pore. A molecule can be made to traverse a pore,i.e. pass from one side of the pore to the other side of the pore bytraveling within the pore, using a variety of methods known to thoseskilled in the art.

In one embodiment, an electrical potential can be used to urge chargedspecies, such as proteins and nucleic acids, through the pore. Themagnitude of the potential, regardless of sign, may be greater thanabout 0.001 V, greater than about 0.01 V, greater than about 0.1 V,greater than about 1 V, greater than about 10 V, greater than about 100V, greater than about 1000 V, or greater than about 10000 V. In otherembodiments, the potential may be between about 0 V and 0.01V, about0.001 V and 0.1 V, about 0.01 V and 1 V, about 0.1 V and 10 V, about 1 Vand 100 V, about 10 V and 1000 V, or about 100 V and 10000 V. It shouldbe understood that the actual voltage used will depend on the specificapplication, and can be determined using routine experimentation. In oneembodiment, the sample chamber contains an electrode 5, such as aAg/AgCl electrode, which is inserted into the solution and in someinstances can apply a negative electrochemical potential to thesolution. A positive electrode 9 may be placed in the reduced pressurechamber 8 to create an electrical potential capable of translocating anegatively charged species 12, such as a nucleic acid, through the pore.In an alternative embodiment, the sample chamber 6 may contain apositive electrode and the reduced pressure chamber 8 may contain anegative electrode, thereby creating an electrical potential capable oftranslocating a positively charged species through the pore. I. In someinstances, the voltage may be kept constant, whereas in other instancesthe voltage may be varied depending, for example in response to datareceived from another aspect of the invention, for instance, the rate ormass to charge ratio of species reaching the detector, or as part of amethod for translocating particular species through the pore.

In another embodiment of the present invention, an applied pressure canbe used to translocate species through the pore. For instance, anapplied hydrostatic pressure difference of about 1 atm between thesample chamber and the vacuum chamber may be used to urge a speciesthrough the pore. In some embodiments, the pressure difference may beless than about 1000 atm, less than about 100 atm, less than about 10atm, less than about 1 atm, less than about 0.1 atm, or less than about0.01 atm. In other embodiments, the pressure difference may be betweenabout 0 atm and 0.1 atm, about 0.01 atm and 1 atm, about 0.1 atm and 10atm, about 1 atm and 100 atm, or about 10 atm and 1000 atm. In yetanother embodiment, the pressure difference may be greater than about1000 atm.

Certain aspects of the invention provide for an ionization source forionizing species within or in proximity to the pore, which may be usedto partially cleave a polymer (or other species) passing through thepore. An “ion” is a species that is charged in some fashion, forexample, positively or negatively. In some cases, the ion may beformally neutrally charged, e.g., as in a zwitterion.

In some embodiments, an electric field is used to ionize a species.Those of ordinary skill in the art will know of methods of creating anelectric field. For example, a large voltage, whose magnitude istypically several kilovolts, can be applied between a first electrodeand a second electrode located at short distance away from the firstelectrode, typically between 1 mm and 10 cm. This applied voltagegenerates strong electric fields at the outlet of the pore and is usedto ionize a species and accelerate it into the mass spectrometer sectionof the device. In some instances, the magnitude of the potential,regardless of sign, may be greater than about 100 V, greater than about500 V, greater than about 1000 V, greater than about 2000 V, greaterthan about 5000 V, greater than about 10000 V, greater than about 50000V, or greater than about 100000 V. In other instances, the potential maybe between about 100 V and 500 V, about 400 V and 1000 V, about 800 Vand 2000 V, about 1500 V and 5000 V, about 4000 V and 10000 V, about8000 V and 50000 V, or about 40000 V and 100000 V. One of ordinary skillin the art would know that voltages are arbitrary and can be determinedusing routine experimentation.

The distance between the first electrode and the second electrode can beless than about 1 mm, less than about 5 mm, less than about 10 mm, lessthan about 50 mm, less than about 100 mm, less than about 500 mm, etc.In another example, the distance between the first electrode and thesecond electrode can be greater than about 500 mm. In other instances,the distance between the first electrode and the second electrode may bebetween about 0.5 mm and 2 mm, about 1 mm and 5 mm, about 2 mm and 10mm, about 5 mm and 25 mm, about 20 mm and 50 mm, about 40 mm and 100 mm,or about 90 mm and 500 mm.

In certain embodiments, the applied voltage generates strong electricfields at the outlet of the pore and is used to ionize the leadingmonomer 13 of a polymer 12, such as the nucleobase of a polynucleotide,and dissociate it from the trailing end of the molecule. The electricfields may also be used to accelerate the charged species 13 into a massspectrometer configured with the pore and ionization source.

Without wishing to be bound by theory, the strong electric fields canionize the leading moiety of a translocating polymer by the mechanism offield ionization and dissociate that moiety from the subsequent bases.In certain instances, the moiety comprises a portion of a monomericunit. In other instances, the moiety comprises an entire monomeric unit.In some examples, the moiety comprises at least one monomeric unit andmay comprise multiple monomeric units. For example, a portion comprisinga portion of nucleotide may be dissociated from a polynucleotide, aportion comprising at least one nucleotide may be dissociated from apolynucleotide, a portion comprising at least one nucleotide and aportion of a second nucleotide may be dissociated from a polynucleotide,a portion comprising multiple nucleotides may be dissociated from apolynucleotide, etc. The membrane electrode ensures that the strongestelectric fields are confined to the vacuum side of the device, and thatthe section of the polymer in the sample compartment remains intact.

In other embodiments, the ionization and/or dissociation of monomersand/or portions of monomers may be promoted by irradiation of the poreor a region near the pore with light, such as laser light. In oneembodiment, the irradiation originates from the vacuum side of thedevice. In another embodiment, the irradiation is incident on the vacuumside of the device. In one embodiment, various monomers of a polymer canbe cleaved from the rest of the polymer at the same bond. For example,each nucleotide in a polynucleotide could be cleaved from thepolynucleotide at the respective sugar-phosphate bond. In anotherexample, each nucleobase could be cleaved from a polynucleotide at thenucleobase-sugar bond. In other instances, each amino acid or part of anamino acid, such as the amino acid side group, could be cleaved from apolypeptide. Alternatively, each sugar within a polysaccharide may becleaved from the polysaccharide. The invention disclosed herein alsocontemplates biopolymers comprising hybrid structures. Such structures,for example peptide-nucleic acids and glycoproteins, are known in theart. The wavelength or wavelengths of the incident light can be chosento target the absorption maxima of a particular bond, for example thesugar-phosphate bond of a polynucleotide, in order to break the bond ata specific position. In one embodiment, an additional incidentwavelength or additional wavelengths can be chosen to ionize eachmonomeric unit, such as a DNA base, as it emerges from the pore on thevacuum side.

Certain embodiments of the invention provide for a particle sourceuseful for ionizing species, for example, a radioactive source. In someinstances the particle source emits a stream of particles from thevacuum side of the pore. In one example, the stream of particles may beincident on the pore or a region near the pore. In one instance, thestream of particles are incident on the vacuum side of the pore. Theparticle stream may be used to fragment a molecule, in some instances asthe molecules emerges from a pore. In some examples, the fragment may becharged, whereas in other examples the fragment may be neutral. In oneembodiment, a molecule may be charged after bombardment by the particlestream, but may otherwise be intact. In some embodiments of theinvention, bombardment by the particle stream fragments a polymer suchthat fragments comprising portions of monomeric units are formed. In oneinstance, a portion of a monomeric unit, at least one monomeric unit, ora portion comprising a plurality of monomeric units are removed from apolymer as they emerge from a pore. The stream of particles emitted bythe particle source may be positively charged, negatively charged, orneutral. In some instances, the particle source may emit argon or xenonatoms or cesium(I) ions. In other instances, the particle source mayemit electrons.

In some embodiments, a system may comprise an electrospray ionizationsource that can be used to ionize a molecule. An electrospray ionizationsource may be operated at any suitable flow rate. For example, a flowrate may be used that is less than about 1000 mL/minute, less than about500 mL/minute, less than about 100 mL/minute, less than about 25mL/minute, etc.

In some aspects of the invention, the mass to charge ratio of an ionizedspecies may be determined using mass spectrometry. In certainembodiments, for example, the mass spectrometer utilizes a mass analyzer11 to separate ions according to the mass to charge ratio. Examples ofmass analyzers include sector field, time-of-flight, quadrupole, triplequadrupole, quadrupole ion trap, linear quadrupole ion trap, Fouriertransform ion cyclotron, etc. Other techniques will be known to thoseskilled in the art. In one embodiment, an ionized species may beaccelerated within a mass spectrometer by applied electric fields, andthe extractor electrode 9 can be perforated so as to allow thetransmission of ions within the spectrometer. Magnetic fields may begenerated in a region 10 of the mass spectrometer through which the ionstravel and induce a deflection in the trajectory of each ion that isrelated to its charge to mass ratio. At the far end of the massspectrometer, a single ion detector array 11 registers the location ofeach ion impingement. The detector array may comprise, for instance, aset of Channeltron (Burle Industries, Inc., Lancaster, Pa.) single iondetectors that are capable of counting ions with high efficiency, insome cases greater than 95% efficiency, and at a high rate, in someinstances exceeding 100 million Hertz.

In some embodiments, the mass spectrometers described herein may operatewith improved efficiency. For example, as discussed, in someembodiments, the invention allows for mass spectrometry of singlemolecules with very little signal-to-noise ratio. In some instances,efficiency may be defined as the number of molecules detected by a massspectrometer divided by the number of molecules entering the massspectrometer. It should be understood that the efficiency is expressedas a fraction less than or equal to 1 and that the fraction may bemultiplied by 100% so as to quantify the efficiency in terms ofpercentile. For example, the efficiency of the mass spectrometer may beat least about 1%, at least about 5%, at least about 10%, at least about15%, at least about 25%, at least about 30%, at least about 40%, atleast about 50%, at least about 60%, at least about 70%, at least about80%, at least about 90%, at least about 95%, at least about 98%, or evenat least about 99%. In some embodiments, the efficiency of a massspectrometer may be determined by measuring detector current (caused bythe detection of target molecules in the spectrometer) as a function ofthe incoming flow rate of the target molecules in a sample. Theconcentration of analyte in a sample may be determined by any number ofknown methods. For example, the analyte may be quantified byspectroscopic techniques (e.g., UV-vis spectrophotometry, NMRspectroscopy, etc.), enzymatic methods (e.g., coupled enzymatic assays,etc.), HPLC, etc.

In some cases, a reduced size of the pore in the mass spectrometer mayallow for increased efficiency of mass spectrometer operation. Forexample, in some embodiments, reducing the number of ions isolated in amass spectrometer can improve signal-to-noise ratio of the massspectrometer. In some instances, a smaller pore diameter may reduce therate at which molecules pass through the pore, and the pore diameter mayeven be such that molecules pass through the pore in “single file”fashion. Without wishing to be bound by any theory, a smaller rate atwhich molecules pass through the pore can lead to a samller number ofions isolated in the mass spectrometer, which can lead to improved massspectrometer efficiency. In some embodiments, a mass spectrometer havinga pore as described herein may operate with higher efficiency than amass spectrometer having a pore larger than the pores described herein.

In certain embodiments, the technique can be insensitive to theorientation of a molecule. Additionally, the technique can beinsensitive to the rate, or a non-uniform rate, at which molecules or amolecule, such as a biopolymer, translocate the pore. For example, inthe case of biopolymer sequencing, the mass of each monomer, or the massof a fragment that corresponds to a monomer, and the order of detectionof the monomers or fragments of monomers are sufficient to determine thesequence of the polymer. In one embodiment, the sequence of massesdetected by the mass spectrometer determines the DNA sequence of thecandidate molecule. For example, if a DNA molecule containing adenine,cytosine, guanine, and thymine were cleaved at the same chemical bondalong the molecule and singly ionized upon entering the massspectrometer, then four different masses would be detected by the massspectrometer, each corresponding to a particular DNA base. In thisexample, the identity of the DNA base may be determined from the mass tocharge ratio. Conversely, if the DNA bases or nucleotides are cleaved atdifferent chemical bonds, the identities of the nucleotides or bases canbe determined by considering the atomic masses that correspond to thepossible DNA base fragments. In this embodiment, the method makes use ofthe known molecular structure of DNA and the fact that a sequence ofnucleotide masses add to form a continuous DNA molecule of a given mass.Alternatively, a tandem mass spectrometer may be employed that utilizesa secondary fragmentation of the initial fragments generated todetermine the identity of a species.

In an embodiment where a DNA molecule is being sequenced using theinvention, the sequence of impingement locations can uniquely identifythe sequence of the DNA molecule as can be seen in FIG. 4. Because themasses of the four common DNA bases, guanine 14, adenine 15, thymine 16,and cytosine 17, differ from one another, accurate sequence information18 may be obtained through mass spectrometry. Those skilled in the artwill recognize that bases other than adenine, cytosine, guanine, andthymine occur naturally within DNA, for example, methylated derivativesof these bases and damage products of these bases, i.e. from ultravioletexposure or exposure to oxidants, for example. The disclosed inventionalso provides for determining these bases as well. A variety ofnon-naturally occurring bases also exist in the art and may beincorporated into a DNA destined for sequencing. Likewise, naturallyoccurring and non-naturally occurring alternative amino acids, i.e.those other than the 20 commonly cited naturally-occurring amino acids,may in part make up a polypeptide.

In certain aspects of the invention, detection of various species isprovided. In some embodiments, the invention can be used to detectbiomarkers within biopolymers. For example, numerous modifications tonucleic acids have been reported to occur in vivo, and many of thesemodifications have been linked to disease, the risk of disease, orvariations in gene expression. For instance, DNA methylation, such as atcytosine residues, can control gene expression in cells. Thus, thepresent invention may be useful for determining the gene expressionprofile of a particular cell, i.e. the epigenetic profile of a patient.DNA methylation may also have a role in suppressing tumor suppressorgenes, and the determination of DNA methylation within tumor suppressorgenes or other regions of the genome may therefore be useful forassaying cancer risk or the specific type of cancer in a patient.

The invention may also be useful in personalized medicine sinceacquiring genetic information about the cancer cells in a subject maylead to selection of a treatment over another treatment. Otherbiomarkers may be useful for determining a subject's risk of disease.For instance, the presence of oxidized DNA bases, such as7,8-dihydro-8-oxoguanine, may be linked to an increased risk of breastcancer and other cancers. Detection of oxidized DNA may also be usefulfor assaying the risk of other diseases for which oxidative stress islinked, including those diseases associated with chronic inflammation.Examples of such diseases include cardiovascular disease, Alzheimer'sdisease, aging, Crohn's disease, etc. Biomarkers may also be found inprotein, for example nitrotyrosine residues, or in polysaccharides. Inother embodiments, the invention may be used to detection of minutequantities of materials. Since the invention allows for massspectrometry of single molecules with very little signal-to-noise ratio,the invention may be used in diagnostic applications for measuring verysmall amounts of analytes in bodily materials such as urine, blood,saliva, feces, mucous, etc. In yet another embodiment, the invention canbe used for the detection of explosives. In another instance, theinvention can be used to detect environmental pollutants or agents.

Polymers that are not biopolymers may also be included as well, invarious embodiments. Examples of such polymers include poly(ethyleneglycol), poly(lactic acid-co-glycolic acid), polyesters, polyamides,polyurethanes, polyacrylates, polyethylenes, polypropylenes,polyanhydrides, etc. or any other molecule comprised of a plurality ofmonomeric units. In some cases, the polymer may be a copolymer, forexample block copolymers or graft copolymers.

U.S. Provisional Patent Application Ser. No. 61/085,480, filed Aug. 1,2008, entitled “System and Methods for Determining Molecules using MassSpectrometry and Related Techniques,” by D. M. Stein, is incorporatedherein by reference in its entirety.

While several embodiments of the present invention have been describedand illustrated herein, those of ordinary skill in the art will readilyenvision a variety of other means and/or structures for performing thefunctions and/or obtaining the results and/or one or more of theadvantages described herein, and each of such variations and/ormodifications is deemed to be within the scope of the present invention.More generally, those skilled in the art will readily appreciate thatall parameters, dimensions, materials, and configurations describedherein are meant to be exemplary and that the actual parameters,dimensions, materials, and/or configurations will depend upon thespecific application or applications for which the teachings of thepresent invention is/are used. Those skilled in the art will recognize,or be able to ascertain using no more than routine experimentation, manyequivalents to the specific embodiments of the invention describedherein. It is, therefore, to be understood that the foregoingembodiments are presented by way of example only and that, within thescope of the appended claims and equivalents thereto, the invention maybe practiced otherwise than as specifically described and claimed. Thepresent invention is directed to each individual feature, system,article, material, kit, and/or method described herein. In addition, anycombination of two or more such features, systems, articles, materials,kits, and/or methods, if such features, systems, articles, materials,kits, and/or methods are not mutually inconsistent, is included withinthe scope of the present invention.

The indefinite articles “a” and “an,” as used herein in thespecification and in the claims, unless clearly indicated to thecontrary, should be understood to mean “at least one.”

The phrase “and/or,” as used herein in the specification and in theclaims, should be understood to mean “either or both” of the elements soconjoined, i.e., elements that are conjunctively present in some casesand disjunctively present in other cases. Other elements may optionallybe present other than the elements specifically identified by the“and/or” clause, whether related or unrelated to those elementsspecifically identified unless clearly indicated to the contrary. Thus,as a non-limiting example, a reference to “A and/or B,” when used inconjunction with open-ended language such as “comprising” can refer, inone embodiment, to A without B (optionally including elements other thanB); in another embodiment, to B without A (optionally including elementsother than A); in yet another embodiment, to both A and B (optionallyincluding other elements); etc.

As used herein in the specification and in the claims, “or” should beunderstood to have the same meaning as “and/or” as defined above. Forexample, when separating items in a list, “or” or “and/or” shall beinterpreted as being inclusive, i.e., the inclusion of at least one, butalso including more than one, of a number or list of elements, and,optionally, additional unlisted items. Only terms clearly indicated tothe contrary, such as “only one of” or “exactly one of,” or, when usedin the claims, “consisting of,” will refer to the inclusion of exactlyone element of a number or list of elements. In general, the term “or”as used herein shall only be interpreted as indicating exclusivealternatives (i.e. “one or the other but not both”) when preceded byterms of exclusivity, such as “either,” “one of,” “only one of,” or“exactly one of.” “Consisting essentially of,” when used in the claims,shall have its ordinary meaning as used in the field of patent law.

As used herein in the specification and in the claims, the phrase “atleast one,” in reference to a list of one or more elements, should beunderstood to mean at least one element selected from any one or more ofthe elements in the list of elements, but not necessarily including atleast one of each and every element specifically listed within the listof elements and not excluding any combinations of elements in the listof elements. This definition also allows that elements may optionally bepresent other than the elements specifically identified within the listof elements to which the phrase “at least one” refers, whether relatedor unrelated to those elements specifically identified. Thus, as anon-limiting example, “at least one of A and B” (or, equivalently, “atleast one of A or B,” or, equivalently “at least one of A and/or B”) canrefer, in one embodiment, to at least one, optionally including morethan one, A, with no B present (and optionally including elements otherthan B); in another embodiment, to at least one, optionally includingmore than one, B, with no A present (and optionally including elementsother than A); in yet another embodiment, to at least one, optionallyincluding more than one, A, and at least one, optionally including morethan one, B (and optionally including other elements); etc.

In the claims, as well as in the specification above, all transitionalphrases such as “comprising,” “including,” “carrying,” “having,”“containing,” “involving,” “holding,” and the like are to be understoodto be open-ended, i.e., to mean including but not limited to. Only thetransitional phrases “consisting of” and “consisting essentially of”shall be closed or semi-closed transitional phrases, respectively, asset forth in the United States Patent Office Manual of Patent ExaminingProcedures, Section 2111.03.

What is claimed:
 1. A method, comprising: passing an polynucleotidethrough a non-naturally occurring pore having a diameter of less thanabout 1 micrometer; and cleaving the polynucleotide in sequence.
 2. Themethod of claim 1, wherein the polynucleotide is DNA.
 3. The method ofclaim 1, wherein the polynucleotide is RNA.
 4. The method of claim 1,wherein the pore has a diameter of less than about 50 nanometers.
 5. Themethod of claim 1, wherein the pore has a diameter of less than about 15nanometers.
 6. The method of claim 1, wherein the pore has a diameter ofless than about 5 nanometers.
 7. The method of claim 1, wherein the porehas a diameter of less than about 2 nanometers.
 8. The method of claim1, wherein the pore separates a first chamber having a pressure at afirst level and a second chamber having a pressure at a second level,the pressure at the first level being less than the pressure at thesecond level.
 9. The method of claim 8, wherein the pressure at a firstlevel is at least 50% less than the pressure at a second level.
 10. Themethod of claim 1, wherein the pore is formed in a solid state material.11. The method of claim 1, wherein the pore is formed in a polymericmaterial.
 12. The method of claim 1, wherein the pore is formed in aceramic material.
 13. The method of claim 1, wherein the polynucleotideis cleaved using a laser or an electric field.
 14. The method of claim1, wherein cleaved portions of the polynucleotide are determined usingmass spectrometry.
 15. The method of claim 1, wherein an electric fieldurges the polynucleotide through the pore.
 16. The method of claim 1,wherein a pressure difference urges the polynucleotide through the pore.17. The method of claim 1, wherein the polynucleotide passes through thepore in single file.
 18. A method according to claim 1, wherein thecleaved polynucleotides are single nucleotides.
 19. A method,comprising: passing an polynucleotide through a non-naturally occurringpore having a diameter of less than about 1 micrometer; and cleaving thepolynucleotide using a laser or an electric field.
 20. The method ofclaim 19, wherein the pore separates a first chamber having a pressureat a first level and a second chamber having a pressure at a secondlevel, the pressure at the first level being less than the pressure atthe second level.
 21. A method according to claim 19, wherein thecleaved polynucleotides are single nucleotides.